noone@mail.com Analysis of Dieting study 16S data % Fri Sep 7 05:46:18 2018

(1.1.1.2.3) Plots of Abundance.

Plots are shown with relation to various combinations of meta data variables and in different graphical representations. Lots of plots here.

(1.1.1.2.3.2) Iterating over all combinations of grouping variables
(1.1.1.2.3.2.1) Grouping variables Sample.type,visit
(1.1.1.2.3.2.2) Iterating over Abundance. profile sorting order
(1.1.1.2.3.2.2.1) Abundance. profile sorting order: average abundance
(1.1.1.2.3.2.2.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.1.1.2.3.2.2.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.1.1.2.3.2.2.2.1.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.2.3.2.2.2.1.1.0) Table 12. Data table used for plots. Data grouped by Sample.type,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.2.3.2.2.2.1.1.0-323805c2f5.1.1.1.2.3.2.2.2.1.1.csv

.record.id Sample.type visit feature Abundance
SM1 patient 1 Bacteroidales 7.837e-01
SM10 patient 3 Bacteroidales 2.396e-01
SM100 patient 4 Bacteroidales 5.483e-01
SM11 patient 2 Bacteroidales 9.084e-01
SM12 patient 1 Bacteroidales 9.279e-01
SM13 patient 1 Bacteroidales 7.549e-01
SM14 patient 1 Bacteroidales 6.361e-02
SM15 control 1 Bacteroidales 4.786e-01
SM16 patient 4 Bacteroidales 3.910e-01
SM17 patient 1 Bacteroidales 8.184e-01
SM18 patient 2 Bacteroidales 7.195e-01
SM19 patient 2 Bacteroidales 2.254e-01
SM2 patient 1 Bacteroidales 8.870e-01
SM20 control 1 Bacteroidales 5.050e-01
SM21 patient 1 Bacteroidales 5.680e-01
SM22 patient 1 Bacteroidales 6.107e-01
SM23 patient 2 Bacteroidales 2.816e-01
SM24 patient 1 Bacteroidales 8.665e-01
SM25 patient 4 Bacteroidales 4.540e-01
SM26 control 1 Bacteroidales 5.338e-01
SM28 control 1 Bacteroidales 2.662e-01
SM29 patient 3 Bacteroidales 9.319e-01
SM3 patient 2 Bacteroidales 3.066e-01
SM30 patient 4 Bacteroidales 6.906e-02
SM31 control 2 Bacteroidales 5.821e-01
SM33 patient 1 Bacteroidales 6.904e-01
SM35 control 1 Bacteroidales 6.847e-01
SM36 patient 4 Bacteroidales 3.219e-04
SM37 control 1 Bacteroidales 4.112e-01
SM38 patient 2 Bacteroidales 9.845e-01
SM39 patient 1 Bacteroidales 9.342e-01
SM40 patient 4 Bacteroidales 7.285e-01
SM41 patient 1 Bacteroidales 5.559e-01
SM42 patient 4 Bacteroidales 7.114e-01
SM43 patient 4 Bacteroidales 7.229e-01
SM44 control 1 Bacteroidales 3.689e-01
SM45 patient 2 Bacteroidales 0.000e+00
SM48 control 1 Bacteroidales 7.186e-01
SM49 patient 1 Bacteroidales 9.322e-01
SM5 patient 3 Bacteroidales 8.376e-01
SM50 patient 3 Bacteroidales 0.000e+00
SM51 patient 4 Bacteroidales 7.147e-01
SM52 patient 1 Bacteroidales 9.827e-02
SM53 patient 2 Bacteroidales 8.029e-01
SM54 patient 3 Bacteroidales 8.090e-01
SM55 control 1 Bacteroidales 7.866e-01
SM56 patient 2 Bacteroidales 7.317e-01
SM57 patient 1 Bacteroidales 9.046e-01
SM58 patient 2 Bacteroidales 7.692e-01
SM59 patient 3 Bacteroidales 5.768e-02
SM60 patient 3 Bacteroidales 8.475e-01
SM62 patient 1 Bacteroidales 9.715e-01
SM63 control 1 Bacteroidales 6.518e-01
SM64 patient 2 Bacteroidales 8.683e-01
SM65 patient 3 Bacteroidales 3.741e-01
SM66 control 1 Bacteroidales 6.462e-01
SM67 patient 4 Bacteroidales 9.138e-01
SM68 patient 4 Bacteroidales 1.705e-01
SM69 patient 4 Bacteroidales 8.374e-01
SM7 control 1 Bacteroidales 2.192e-01
SM70 control 1 Bacteroidales 5.637e-01
SM71 patient 3 Bacteroidales 9.175e-01
SM72 control 1 Bacteroidales 2.778e-01
SM73 patient 1 Bacteroidales 8.563e-01
SM74 control 2 Bacteroidales 9.231e-02
SM75 patient 3 Bacteroidales 2.377e-03
SM76 control 1 Bacteroidales 8.224e-01
SM77 patient 2 Bacteroidales 7.635e-01
SM79 patient 2 Bacteroidales 8.495e-01
SM8 patient 1 Bacteroidales 8.250e-01
SM81 control 1 Bacteroidales 0.000e+00
SM82 patient 4 Bacteroidales 9.555e-01
SM83 patient 1 Bacteroidales 8.254e-01
SM84 patient 1 Bacteroidales 8.858e-01
SM86 patient 2 Bacteroidales 2.792e-03
SM87 patient 1 Bacteroidales 8.668e-01
SM88 patient 2 Bacteroidales 8.385e-01
SM89 control 1 Bacteroidales 8.778e-01
SM9 patient 2 Bacteroidales 6.635e-01
SM90 patient 2 Bacteroidales 6.176e-01
SM91 patient 3 Bacteroidales 7.223e-01
SM92 patient 3 Bacteroidales 8.864e-01
SM93 patient 1 Bacteroidales 7.781e-01
SM95 control 1 Bacteroidales 5.366e-01
SM96 patient 1 Bacteroidales 6.376e-01
SM98 patient 3 Bacteroidales 8.378e-01
SM99 patient 3 Bacteroidales 6.951e-01
SM1 patient 1 Clostridiales 1.709e-01
SM10 patient 3 Clostridiales 7.097e-01
SM100 patient 4 Clostridiales 4.044e-01
SM11 patient 2 Clostridiales 6.923e-02
SM12 patient 1 Clostridiales 6.299e-02
SM13 patient 1 Clostridiales 1.670e-01
SM14 patient 1 Clostridiales 3.018e-01
SM15 control 1 Clostridiales 4.844e-01
SM16 patient 4 Clostridiales 5.717e-01
SM17 patient 1 Clostridiales 1.038e-01
SM18 patient 2 Clostridiales 9.552e-02
SM19 patient 2 Clostridiales 7.154e-01
SM2 patient 1 Clostridiales 2.821e-02
SM20 control 1 Clostridiales 4.550e-01
SM21 patient 1 Clostridiales 3.925e-01
SM22 patient 1 Clostridiales 2.891e-01
SM23 patient 2 Clostridiales 1.659e-03
SM24 patient 1 Clostridiales 8.129e-02
SM25 patient 4 Clostridiales 5.006e-01
SM26 control 1 Clostridiales 2.131e-01
SM28 control 1 Clostridiales 6.583e-01
SM29 patient 3 Clostridiales 5.931e-02
SM3 patient 2 Clostridiales 6.225e-01
SM30 patient 4 Clostridiales 6.076e-01
SM31 control 2 Clostridiales 3.188e-01
SM33 patient 1 Clostridiales 4.996e-02
SM35 control 1 Clostridiales 1.664e-01
SM36 patient 4 Clostridiales 7.193e-01
SM37 control 1 Clostridiales 4.996e-01
SM38 patient 2 Clostridiales 1.115e-02
SM39 patient 1 Clostridiales 4.334e-02
SM40 patient 4 Clostridiales 1.535e-01
SM41 patient 1 Clostridiales 1.723e-01
SM42 patient 4 Clostridiales 2.559e-01
SM43 patient 4 Clostridiales 1.955e-01
SM44 control 1 Clostridiales 5.344e-01
SM45 patient 2 Clostridiales 0.000e+00
SM48 control 1 Clostridiales 2.252e-01
SM49 patient 1 Clostridiales 5.216e-02
SM5 patient 3 Clostridiales 9.120e-02
SM50 patient 3 Clostridiales 7.065e-01
SM51 patient 4 Clostridiales 1.970e-01
SM52 patient 1 Clostridiales 6.445e-01
SM53 patient 2 Clostridiales 1.491e-01
SM54 patient 3 Clostridiales 1.726e-01
SM55 control 1 Clostridiales 1.877e-01
SM56 patient 2 Clostridiales 2.125e-01
SM57 patient 1 Clostridiales 8.819e-02
SM58 patient 2 Clostridiales 1.200e-01
SM59 patient 3 Clostridiales 7.978e-01
SM60 patient 3 Clostridiales 6.399e-02
SM62 patient 1 Clostridiales 2.529e-02
SM63 control 1 Clostridiales 2.766e-01
SM64 patient 2 Clostridiales 7.026e-02
SM65 patient 3 Clostridiales 5.640e-01
SM66 control 1 Clostridiales 3.152e-01
SM67 patient 4 Clostridiales 7.164e-02
SM68 patient 4 Clostridiales 5.874e-01
SM69 patient 4 Clostridiales 1.229e-01
SM7 control 1 Clostridiales 6.268e-01
SM70 control 1 Clostridiales 3.025e-01
SM71 patient 3 Clostridiales 5.366e-02
SM72 control 1 Clostridiales 1.571e-01
SM73 patient 1 Clostridiales 9.994e-02
SM74 control 2 Clostridiales 7.925e-01
SM75 patient 3 Clostridiales 8.122e-01
SM76 control 1 Clostridiales 1.502e-01
SM77 patient 2 Clostridiales 1.921e-01
SM79 patient 2 Clostridiales 1.412e-01
SM8 patient 1 Clostridiales 1.294e-01
SM81 control 1 Clostridiales 3.292e-01
SM82 patient 4 Clostridiales 2.914e-02
SM83 patient 1 Clostridiales 1.565e-01
SM84 patient 1 Clostridiales 5.785e-02
SM86 patient 2 Clostridiales 8.889e-01
SM87 patient 1 Clostridiales 7.040e-02
SM88 patient 2 Clostridiales 1.247e-01
SM89 control 1 Clostridiales 6.822e-02
SM9 patient 2 Clostridiales 7.939e-02
SM90 patient 2 Clostridiales 2.991e-01
SM91 patient 3 Clostridiales 2.006e-01
SM92 patient 3 Clostridiales 8.090e-02
SM93 patient 1 Clostridiales 1.938e-01
SM95 control 1 Clostridiales 3.756e-01
SM96 patient 1 Clostridiales 2.363e-01
SM98 patient 3 Clostridiales 5.983e-02
SM99 patient 3 Clostridiales 2.487e-01
SM1 patient 1 Lactobacillales 4.329e-04
SM10 patient 3 Lactobacillales 4.240e-04
SM100 patient 4 Lactobacillales 3.077e-04
SM11 patient 2 Lactobacillales 6.567e-04
SM12 patient 1 Lactobacillales 8.853e-05
SM13 patient 1 Lactobacillales 0.000e+00
SM14 patient 1 Lactobacillales 1.905e-01
SM15 control 1 Lactobacillales 1.557e-03
SM16 patient 4 Lactobacillales 4.875e-03
SM17 patient 1 Lactobacillales 1.241e-03
SM18 patient 2 Lactobacillales 1.242e-02
SM19 patient 2 Lactobacillales 1.388e-03
SM2 patient 1 Lactobacillales 7.278e-02
SM20 control 1 Lactobacillales 2.955e-03
SM21 patient 1 Lactobacillales 2.690e-03
SM22 patient 1 Lactobacillales 3.071e-03
SM23 patient 2 Lactobacillales 7.105e-01
SM24 patient 1 Lactobacillales 6.431e-04
SM25 patient 4 Lactobacillales 7.765e-03
SM26 control 1 Lactobacillales 7.612e-02
SM28 control 1 Lactobacillales 0.000e+00
SM29 patient 3 Lactobacillales 0.000e+00
SM3 patient 2 Lactobacillales 8.146e-03
SM30 patient 4 Lactobacillales 7.637e-03
SM31 control 2 Lactobacillales 3.236e-03
SM33 patient 1 Lactobacillales 7.868e-04

(1.1.1.2.3.2.2.2.1.1.1) Widget 11. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Sample.type,visit. Click to see HTML widget file in full window: ./1.1.1.2.3.2.2.2.1.1.1-32346f2bd5cDynamic.Pivot.Table.html

(1.1.1.2.3.2.2.2.1.1.1) Widget 12. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Sample.type,visit. Click to see HTML widget file in full window: ./1.1.1.2.3.2.2.2.1.1.1-3233e785abeDynamic.Pivot.Table.html

(1.1.1.2.3.2.2.2.1.1.1) Table 13. Summary table. Data grouped by Sample.type,visit. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.2.3.2.2.2.1.1.1-32342cf715c.1.1.1.2.3.2.2.2.1.1.csv

feature Sample.type visit mean sd median incidence
Bacteroidales control 1 5.194e-01 0.2317911 5.352e-01 0.94444
Bacteroidales control 2 3.372e-01 0.3463494 3.372e-01 1.00000
Bacteroidales patient 1 7.410e-01 0.2398655 8.250e-01 1.00000
Bacteroidales patient 2 6.078e-01 0.3172098 7.317e-01 0.94118
Bacteroidales patient 3 5.828e-01 0.3640601 7.656e-01 0.92857
Bacteroidales patient 4 5.552e-01 0.3170185 7.114e-01 1.00000
Clostridiales control 1 3.347e-01 0.1738358 3.088e-01 1.00000
Clostridiales control 2 5.556e-01 0.3349573 5.556e-01 1.00000
Clostridiales patient 1 1.573e-01 0.1434097 1.038e-01 1.00000
Clostridiales patient 2 2.231e-01 0.2636541 1.247e-01 0.94118
Clostridiales patient 3 3.301e-01 0.3104167 1.866e-01 1.00000
Clostridiales patient 4 3.397e-01 0.2343851 2.559e-01 1.00000
Lactobacillales control 1 2.388e-02 0.0664402 8.704e-04 0.88889
Lactobacillales control 2 5.546e-03 0.0032666 5.546e-03 1.00000
Lactobacillales patient 1 1.344e-02 0.0415706 7.868e-04 0.86957
Lactobacillales patient 2 1.031e-01 0.2876828 1.388e-03 0.94118
Lactobacillales patient 3 5.952e-03 0.0175909 7.366e-04 0.78571
Lactobacillales patient 4 2.825e-03 0.0038509 4.625e-04 1.00000
Erysipelotrichales control 1 9.927e-03 0.0166163 4.025e-03 0.88889
Erysipelotrichales control 2 8.243e-03 0.0037885 8.243e-03 1.00000
Erysipelotrichales patient 1 2.643e-02 0.0794431 8.445e-03 0.91304
Erysipelotrichales patient 2 5.831e-03 0.0085525 2.776e-03 0.88235
Erysipelotrichales patient 3 1.902e-02 0.0273994 6.057e-03 1.00000
Erysipelotrichales patient 4 3.024e-02 0.0688782 4.538e-03 1.00000
Selenomonadales control 1 2.523e-02 0.0595107 2.399e-03 0.94444
Selenomonadales control 2 1.364e-02 0.0178986 1.364e-02 1.00000
Selenomonadales patient 1 6.142e-03 0.0130034 1.513e-03 0.91304
Selenomonadales patient 2 3.053e-02 0.0575852 4.619e-03 0.76471
Selenomonadales patient 3 1.399e-02 0.0230823 5.640e-03 0.78571
Selenomonadales patient 4 7.487e-03 0.0083573 5.871e-03 0.92308
Enterobacteriales control 1 1.802e-02 0.0724385 3.219e-04 0.61111
Enterobacteriales control 2 3.389e-03 0.0030767 3.389e-03 1.00000
Enterobacteriales patient 1 1.775e-02 0.0568164 0.000e+00 0.47826
Enterobacteriales patient 2 2.574e-03 0.0057255 2.227e-04 0.64706
Enterobacteriales patient 3 6.689e-03 0.0156508 7.915e-04 0.71429
Enterobacteriales patient 4 1.651e-02 0.0281531 1.743e-03 0.69231
Burkholderiales control 1 1.205e-02 0.0275947 2.167e-03 0.83333
Burkholderiales control 2 0.000e+00 0.0000000 0.000e+00 0.00000
Burkholderiales patient 1 9.077e-03 0.0145733 1.809e-03 0.78261
Burkholderiales patient 2 1.203e-02 0.0173458 0.000e+00 0.47059
Burkholderiales patient 3 5.595e-03 0.0126940 0.000e+00 0.28571
Burkholderiales patient 4 1.047e-02 0.0243840 0.000e+00 0.46154
Unclassified_Bacteria control 1 1.364e-02 0.0114079 1.054e-02 1.00000
Unclassified_Bacteria control 2 2.617e-02 0.0324305 2.617e-02 1.00000
Unclassified_Bacteria patient 1 8.586e-03 0.0185047 3.658e-03 0.95652
Unclassified_Bacteria patient 2 2.162e-03 0.0019168 1.958e-03 0.88235
Unclassified_Bacteria patient 3 3.391e-03 0.0031220 2.417e-03 1.00000
Unclassified_Bacteria patient 4 4.709e-03 0.0065490 1.415e-03 1.00000
Unclassified_Firmicutes control 1 8.036e-03 0.0109414 3.210e-03 1.00000
Unclassified_Firmicutes control 2 1.259e-02 0.0057974 1.259e-02 1.00000
Unclassified_Firmicutes patient 1 2.429e-03 0.0033961 8.410e-04 0.86957
Unclassified_Firmicutes patient 2 5.485e-03 0.0092386 7.794e-04 0.76471
Unclassified_Firmicutes patient 3 9.325e-03 0.0180189 1.689e-03 1.00000
Unclassified_Firmicutes patient 4 4.155e-03 0.0066088 9.688e-04 0.92308
Pasteurellales control 1 9.234e-04 0.0012789 4.058e-04 0.66667
Pasteurellales control 2 4.910e-03 0.0069438 4.910e-03 0.50000
Pasteurellales patient 1 5.592e-04 0.0017216 0.000e+00 0.34783
Pasteurellales patient 2 1.346e-03 0.0020465 1.920e-04 0.64706
Pasteurellales patient 3 7.072e-03 0.0144512 5.086e-04 0.50000
Pasteurellales patient 4 2.197e-02 0.0531504 2.236e-04 0.76923
Bifidobacteriales control 1 1.565e-02 0.0449947 1.592e-03 0.77778
Bifidobacteriales control 2 6.749e-03 0.0089723 6.749e-03 1.00000
Bifidobacteriales patient 1 1.791e-03 0.0046990 3.015e-04 0.65217
Bifidobacteriales patient 2 7.266e-04 0.0018724 7.192e-05 0.58824
Bifidobacteriales patient 3 3.665e-03 0.0070439 1.831e-04 0.57143
Bifidobacteriales patient 4 2.813e-03 0.0050442 2.231e-04 0.61538
Verrucomicrobiales control 1 2.550e-03 0.0051198 0.000e+00 0.38889
Verrucomicrobiales control 2 2.136e-02 0.0292859 2.136e-02 1.00000
Verrucomicrobiales patient 1 1.056e-02 0.0368541 0.000e+00 0.34783
Verrucomicrobiales patient 2 3.903e-04 0.0011122 0.000e+00 0.11765
Verrucomicrobiales patient 3 5.727e-04 0.0018438 0.000e+00 0.14286
Verrucomicrobiales patient 4 2.846e-05 0.0001026 0.000e+00 0.07692
Rhizobiales control 1 6.352e-03 0.0060510 7.039e-03 0.88889
Rhizobiales control 2 2.455e-03 0.0034719 2.455e-03 0.50000
Rhizobiales patient 1 1.805e-03 0.0030577 3.015e-04 0.56522
Rhizobiales patient 2 2.749e-03 0.0052004 3.863e-04 0.64706
Rhizobiales patient 3 6.442e-04 0.0020172 0.000e+00 0.21429
Rhizobiales patient 4 1.296e-03 0.0031555 0.000e+00 0.46154

(1.1.1.2.3.2.2.2.1.1.1) Figure 47. Abundance. Data grouped by Sample.type,visit. bar_stacked plot. Image file: plots/323ed436fb.svg.

(1.1.1.2.3.2.2.2.1.1.1) Figure 48. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/32344305c44.svg.

(1.1.1.2.3.2.2.2.1.1.1) Figure 49. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/323189339b7.svg.

(1.1.1.2.3.2.2.2.1.1.1) Figure 50. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/323600dc92b.svg.

(1.1.1.2.3.2.2.2.1.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.2.3.2.2.2.1.2.1) Figure 51. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/3234e5c84db.svg.

(1.1.1.2.3.2.2.2.1.2.1) Figure 52. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/323378ca42a.svg.

(1.1.1.2.3.2.2.2.1.2.1) Figure 53. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/32330c8c729.svg.

(1.1.1.2.3.2.2.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.1.1.2.3.2.2.2.2.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.2.3.2.2.2.2.1.1) Figure 54. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/3232e4ea6ad.svg.

(1.1.1.2.3.2.2.2.2.1.1) Figure 55. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/3237aff9273.svg.

(1.1.1.2.3.2.2.2.2.1.1) Figure 56. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/323338193e9.svg.

(1.1.1.2.3.2.2.2.2.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.2.3.2.2.2.2.2.1) Figure 57. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/3233b50a2b3.svg.

(1.1.1.2.3.2.2.2.2.2.1) Figure 58. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/323529ed0a.svg.

(1.1.1.2.3.2.2.2.2.2.1) Figure 59. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/3232620d6c.svg.

(1.1.1.2.3.2.3) Grouping variables Sample.type.Drug.Before,visit
(1.1.1.2.3.2.4) Iterating over Abundance. profile sorting order
(1.1.1.2.3.2.4.1) Abundance. profile sorting order: average abundance
(1.1.1.2.3.2.4.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.1.1.2.3.2.4.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.1.1.2.3.2.4.2.1.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.2.3.2.4.2.1.1.0) Table 14. Data table used for plots. Data grouped by Sample.type.Drug.Before,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.2.3.2.4.2.1.1.0-3236b4f1a01.1.1.1.2.3.2.4.2.1.1.csv

.record.id Sample.type.Drug.Before visit feature Abundance
SM1 patient TRUE . 1 Bacteroidales 7.837e-01
SM10 patient TRUE . 3 Bacteroidales 2.396e-01
SM100 patient TRUE . 4 Bacteroidales 5.483e-01
SM11 patient TRUE . 2 Bacteroidales 9.084e-01
SM12 patient TRUE . 1 Bacteroidales 9.279e-01
SM13 patient FALSE . 1 Bacteroidales 7.549e-01
SM14 patient FALSE . 1 Bacteroidales 6.361e-02
SM15 1 1 Bacteroidales 4.786e-01
SM16 patient FALSE . 4 Bacteroidales 3.910e-01
SM17 patient TRUE . 1 Bacteroidales 8.184e-01
SM18 patient FALSE . 2 Bacteroidales 7.195e-01
SM19 patient FALSE . 2 Bacteroidales 2.254e-01
SM2 patient FALSE . 1 Bacteroidales 8.870e-01
SM20 1 1 Bacteroidales 5.050e-01
SM21 patient FALSE . 1 Bacteroidales 5.680e-01
SM22 patient TRUE . 1 Bacteroidales 6.107e-01
SM23 patient TRUE . 2 Bacteroidales 2.816e-01
SM24 patient FALSE . 1 Bacteroidales 8.665e-01
SM25 patient FALSE . 4 Bacteroidales 4.540e-01
SM26 1 1 Bacteroidales 5.338e-01
SM28 1 1 Bacteroidales 2.662e-01
SM29 patient TRUE . 3 Bacteroidales 9.319e-01
SM3 patient TRUE . 2 Bacteroidales 3.066e-01
SM30 patient TRUE . 4 Bacteroidales 6.906e-02
SM31 1 2 Bacteroidales 5.821e-01
SM33 patient TRUE . 1 Bacteroidales 6.904e-01
SM35 1 1 Bacteroidales 6.847e-01
SM36 patient FALSE . 4 Bacteroidales 3.219e-04
SM37 1 1 Bacteroidales 4.112e-01
SM38 patient TRUE . 2 Bacteroidales 9.845e-01
SM39 patient FALSE . 1 Bacteroidales 9.342e-01
SM40 patient FALSE . 4 Bacteroidales 7.285e-01
SM41 patient TRUE . 1 Bacteroidales 5.559e-01
SM42 patient FALSE . 4 Bacteroidales 7.114e-01
SM43 patient TRUE . 4 Bacteroidales 7.229e-01
SM44 1 1 Bacteroidales 3.689e-01
SM45 patient FALSE . 2 Bacteroidales 0.000e+00
SM48 1 1 Bacteroidales 7.186e-01
SM49 patient TRUE . 1 Bacteroidales 9.322e-01
SM5 patient TRUE . 3 Bacteroidales 8.376e-01
SM50 patient FALSE . 3 Bacteroidales 0.000e+00
SM51 patient TRUE . 4 Bacteroidales 7.147e-01
SM52 patient FALSE . 1 Bacteroidales 9.827e-02
SM53 patient TRUE . 2 Bacteroidales 8.029e-01
SM54 patient TRUE . 3 Bacteroidales 8.090e-01
SM55 1 1 Bacteroidales 7.866e-01
SM56 patient TRUE . 2 Bacteroidales 7.317e-01
SM57 patient TRUE . 1 Bacteroidales 9.046e-01
SM58 patient FALSE . 2 Bacteroidales 7.692e-01
SM59 patient FALSE . 3 Bacteroidales 5.768e-02
SM60 patient TRUE . 3 Bacteroidales 8.475e-01
SM62 patient TRUE . 1 Bacteroidales 9.715e-01
SM63 1 1 Bacteroidales 6.518e-01
SM64 patient TRUE . 2 Bacteroidales 8.683e-01
SM65 patient TRUE . 3 Bacteroidales 3.741e-01
SM66 1 1 Bacteroidales 6.462e-01
SM67 patient TRUE . 4 Bacteroidales 9.138e-01
SM68 patient FALSE . 4 Bacteroidales 1.705e-01
SM69 patient TRUE . 4 Bacteroidales 8.374e-01
SM7 1 1 Bacteroidales 2.192e-01
SM70 1 1 Bacteroidales 5.637e-01
SM71 patient TRUE . 3 Bacteroidales 9.175e-01
SM72 1 1 Bacteroidales 2.778e-01
SM73 patient FALSE . 1 Bacteroidales 8.563e-01
SM74 1 2 Bacteroidales 9.231e-02
SM75 patient FALSE . 3 Bacteroidales 2.377e-03
SM76 1 1 Bacteroidales 8.224e-01
SM77 patient TRUE . 2 Bacteroidales 7.635e-01
SM79 patient FALSE . 2 Bacteroidales 8.495e-01
SM8 patient FALSE . 1 Bacteroidales 8.250e-01
SM81 1 1 Bacteroidales 0.000e+00
SM82 patient TRUE . 4 Bacteroidales 9.555e-01
SM83 patient TRUE . 1 Bacteroidales 8.254e-01
SM84 patient TRUE . 1 Bacteroidales 8.858e-01
SM86 patient TRUE . 2 Bacteroidales 2.792e-03
SM87 patient TRUE . 1 Bacteroidales 8.668e-01
SM88 patient TRUE . 2 Bacteroidales 8.385e-01
SM89 1 1 Bacteroidales 8.778e-01
SM9 patient FALSE . 2 Bacteroidales 6.635e-01
SM90 patient FALSE . 2 Bacteroidales 6.176e-01
SM91 patient TRUE . 3 Bacteroidales 7.223e-01
SM92 patient FALSE . 3 Bacteroidales 8.864e-01
SM93 patient TRUE . 1 Bacteroidales 7.781e-01
SM95 1 1 Bacteroidales 5.366e-01
SM96 patient FALSE . 1 Bacteroidales 6.376e-01
SM98 patient FALSE . 3 Bacteroidales 8.378e-01
SM99 patient FALSE . 3 Bacteroidales 6.951e-01
SM1 patient TRUE . 1 Clostridiales 1.709e-01
SM10 patient TRUE . 3 Clostridiales 7.097e-01
SM100 patient TRUE . 4 Clostridiales 4.044e-01
SM11 patient TRUE . 2 Clostridiales 6.923e-02
SM12 patient TRUE . 1 Clostridiales 6.299e-02
SM13 patient FALSE . 1 Clostridiales 1.670e-01
SM14 patient FALSE . 1 Clostridiales 3.018e-01
SM15 1 1 Clostridiales 4.844e-01
SM16 patient FALSE . 4 Clostridiales 5.717e-01
SM17 patient TRUE . 1 Clostridiales 1.038e-01
SM18 patient FALSE . 2 Clostridiales 9.552e-02
SM19 patient FALSE . 2 Clostridiales 7.154e-01
SM2 patient FALSE . 1 Clostridiales 2.821e-02
SM20 1 1 Clostridiales 4.550e-01
SM21 patient FALSE . 1 Clostridiales 3.925e-01
SM22 patient TRUE . 1 Clostridiales 2.891e-01
SM23 patient TRUE . 2 Clostridiales 1.659e-03
SM24 patient FALSE . 1 Clostridiales 8.129e-02
SM25 patient FALSE . 4 Clostridiales 5.006e-01
SM26 1 1 Clostridiales 2.131e-01
SM28 1 1 Clostridiales 6.583e-01
SM29 patient TRUE . 3 Clostridiales 5.931e-02
SM3 patient TRUE . 2 Clostridiales 6.225e-01
SM30 patient TRUE . 4 Clostridiales 6.076e-01
SM31 1 2 Clostridiales 3.188e-01
SM33 patient TRUE . 1 Clostridiales 4.996e-02
SM35 1 1 Clostridiales 1.664e-01
SM36 patient FALSE . 4 Clostridiales 7.193e-01
SM37 1 1 Clostridiales 4.996e-01
SM38 patient TRUE . 2 Clostridiales 1.115e-02
SM39 patient FALSE . 1 Clostridiales 4.334e-02
SM40 patient FALSE . 4 Clostridiales 1.535e-01
SM41 patient TRUE . 1 Clostridiales 1.723e-01
SM42 patient FALSE . 4 Clostridiales 2.559e-01
SM43 patient TRUE . 4 Clostridiales 1.955e-01
SM44 1 1 Clostridiales 5.344e-01
SM45 patient FALSE . 2 Clostridiales 0.000e+00
SM48 1 1 Clostridiales 2.252e-01
SM49 patient TRUE . 1 Clostridiales 5.216e-02
SM5 patient TRUE . 3 Clostridiales 9.120e-02
SM50 patient FALSE . 3 Clostridiales 7.065e-01
SM51 patient TRUE . 4 Clostridiales 1.970e-01
SM52 patient FALSE . 1 Clostridiales 6.445e-01
SM53 patient TRUE . 2 Clostridiales 1.491e-01
SM54 patient TRUE . 3 Clostridiales 1.726e-01
SM55 1 1 Clostridiales 1.877e-01
SM56 patient TRUE . 2 Clostridiales 2.125e-01
SM57 patient TRUE . 1 Clostridiales 8.819e-02
SM58 patient FALSE . 2 Clostridiales 1.200e-01
SM59 patient FALSE . 3 Clostridiales 7.978e-01
SM60 patient TRUE . 3 Clostridiales 6.399e-02
SM62 patient TRUE . 1 Clostridiales 2.529e-02
SM63 1 1 Clostridiales 2.766e-01
SM64 patient TRUE . 2 Clostridiales 7.026e-02
SM65 patient TRUE . 3 Clostridiales 5.640e-01
SM66 1 1 Clostridiales 3.152e-01
SM67 patient TRUE . 4 Clostridiales 7.164e-02
SM68 patient FALSE . 4 Clostridiales 5.874e-01
SM69 patient TRUE . 4 Clostridiales 1.229e-01
SM7 1 1 Clostridiales 6.268e-01
SM70 1 1 Clostridiales 3.025e-01
SM71 patient TRUE . 3 Clostridiales 5.366e-02
SM72 1 1 Clostridiales 1.571e-01
SM73 patient FALSE . 1 Clostridiales 9.994e-02
SM74 1 2 Clostridiales 7.925e-01
SM75 patient FALSE . 3 Clostridiales 8.122e-01
SM76 1 1 Clostridiales 1.502e-01
SM77 patient TRUE . 2 Clostridiales 1.921e-01
SM79 patient FALSE . 2 Clostridiales 1.412e-01
SM8 patient FALSE . 1 Clostridiales 1.294e-01
SM81 1 1 Clostridiales 3.292e-01
SM82 patient TRUE . 4 Clostridiales 2.914e-02
SM83 patient TRUE . 1 Clostridiales 1.565e-01
SM84 patient TRUE . 1 Clostridiales 5.785e-02
SM86 patient TRUE . 2 Clostridiales 8.889e-01
SM87 patient TRUE . 1 Clostridiales 7.040e-02
SM88 patient TRUE . 2 Clostridiales 1.247e-01
SM89 1 1 Clostridiales 6.822e-02
SM9 patient FALSE . 2 Clostridiales 7.939e-02
SM90 patient FALSE . 2 Clostridiales 2.991e-01
SM91 patient TRUE . 3 Clostridiales 2.006e-01
SM92 patient FALSE . 3 Clostridiales 8.090e-02
SM93 patient TRUE . 1 Clostridiales 1.938e-01
SM95 1 1 Clostridiales 3.756e-01
SM96 patient FALSE . 1 Clostridiales 2.363e-01
SM98 patient FALSE . 3 Clostridiales 5.983e-02
SM99 patient FALSE . 3 Clostridiales 2.487e-01
SM1 patient TRUE . 1 Lactobacillales 4.329e-04
SM10 patient TRUE . 3 Lactobacillales 4.240e-04
SM100 patient TRUE . 4 Lactobacillales 3.077e-04
SM11 patient TRUE . 2 Lactobacillales 6.567e-04
SM12 patient TRUE . 1 Lactobacillales 8.853e-05
SM13 patient FALSE . 1 Lactobacillales 0.000e+00
SM14 patient FALSE . 1 Lactobacillales 1.905e-01
SM15 1 1 Lactobacillales 1.557e-03
SM16 patient FALSE . 4 Lactobacillales 4.875e-03
SM17 patient TRUE . 1 Lactobacillales 1.241e-03
SM18 patient FALSE . 2 Lactobacillales 1.242e-02
SM19 patient FALSE . 2 Lactobacillales 1.388e-03
SM2 patient FALSE . 1 Lactobacillales 7.278e-02
SM20 1 1 Lactobacillales 2.955e-03
SM21 patient FALSE . 1 Lactobacillales 2.690e-03
SM22 patient TRUE . 1 Lactobacillales 3.071e-03
SM23 patient TRUE . 2 Lactobacillales 7.105e-01
SM24 patient FALSE . 1 Lactobacillales 6.431e-04
SM25 patient FALSE . 4 Lactobacillales 7.765e-03
SM26 1 1 Lactobacillales 7.612e-02
SM28 1 1 Lactobacillales 0.000e+00
SM29 patient TRUE . 3 Lactobacillales 0.000e+00
SM3 patient TRUE . 2 Lactobacillales 8.146e-03
SM30 patient TRUE . 4 Lactobacillales 7.637e-03
SM31 1 2 Lactobacillales 3.236e-03
SM33 patient TRUE . 1 Lactobacillales 7.868e-04

(1.1.1.2.3.2.4.2.1.1.1) Widget 13. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Sample.type.Drug.Before,visit. Click to see HTML widget file in full window: ./1.1.1.2.3.2.4.2.1.1.1-323725b49b7Dynamic.Pivot.Table.html

(1.1.1.2.3.2.4.2.1.1.1) Widget 14. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Sample.type.Drug.Before,visit. Click to see HTML widget file in full window: ./1.1.1.2.3.2.4.2.1.1.1-3237b3b4544Dynamic.Pivot.Table.html

(1.1.1.2.3.2.4.2.1.1.1) Table 15. Summary table. Data grouped by Sample.type.Drug.Before,visit. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.2.3.2.4.2.1.1.1-3232dd2d2da.1.1.1.2.3.2.4.2.1.1.csv

feature Sample.type.Drug.Before visit mean sd median incidence
Bacteroidales 1 1 5.194e-01 0.2317911 5.352e-01 0.9444
Bacteroidales 1 2 3.372e-01 0.3463494 3.372e-01 1.0000
Bacteroidales patient FALSE . 1 6.491e-01 0.3202663 7.900e-01 1.0000
Bacteroidales patient FALSE . 2 5.492e-01 0.3140597 6.635e-01 0.8571
Bacteroidales patient FALSE . 3 4.132e-01 0.4357994 3.764e-01 0.8333
Bacteroidales patient FALSE . 4 4.093e-01 0.2897517 4.225e-01 1.0000
Bacteroidales patient TRUE . 1 8.116e-01 0.1269502 8.254e-01 1.0000
Bacteroidales patient TRUE . 2 6.489e-01 0.3295217 7.832e-01 1.0000
Bacteroidales patient TRUE . 3 7.099e-01 0.2595538 8.233e-01 1.0000
Bacteroidales patient TRUE . 4 6.803e-01 0.3024840 7.229e-01 1.0000
Clostridiales 1 1 3.347e-01 0.1738358 3.088e-01 1.0000
Clostridiales 1 2 5.556e-01 0.3349573 5.556e-01 1.0000
Clostridiales patient FALSE . 1 2.124e-01 0.1911962 1.482e-01 1.0000
Clostridiales patient FALSE . 2 2.072e-01 0.2416660 1.200e-01 0.8571
Clostridiales patient FALSE . 3 4.510e-01 0.3597100 4.776e-01 1.0000
Clostridiales patient FALSE . 4 4.647e-01 0.2158834 5.361e-01 1.0000
Clostridiales patient TRUE . 1 1.149e-01 0.0761953 8.819e-02 1.0000
Clostridiales patient TRUE . 2 2.342e-01 0.2903648 1.369e-01 1.0000
Clostridiales patient TRUE . 3 2.394e-01 0.2541613 1.319e-01 1.0000
Clostridiales patient TRUE . 4 2.326e-01 0.2049713 1.955e-01 1.0000
Lactobacillales 1 1 2.388e-02 0.0664402 8.704e-04 0.8889
Lactobacillales 1 2 5.546e-03 0.0032666 5.546e-03 1.0000
Lactobacillales patient FALSE . 1 2.930e-02 0.0610415 1.463e-03 0.9000
Lactobacillales patient FALSE . 2 1.457e-01 0.3766353 1.645e-03 1.0000
Lactobacillales patient FALSE . 3 1.300e-02 0.0264523 1.059e-03 0.8333
Lactobacillales patient FALSE . 4 4.254e-03 0.0046711 2.759e-03 1.0000
Lactobacillales patient TRUE . 1 1.230e-03 0.0015603 4.329e-04 0.8462
Lactobacillales patient TRUE . 2 7.318e-02 0.2239508 5.789e-04 0.9000
Lactobacillales patient TRUE . 3 6.641e-04 0.0005471 6.782e-04 0.7500
Lactobacillales patient TRUE . 4 1.600e-03 0.0027715 3.077e-04 1.0000
Erysipelotrichales 1 1 9.927e-03 0.0166163 4.025e-03 0.8889
Erysipelotrichales 1 2 8.243e-03 0.0037885 8.243e-03 1.0000
Erysipelotrichales patient FALSE . 1 4.869e-02 0.1197808 9.058e-03 1.0000
Erysipelotrichales patient FALSE . 2 4.388e-03 0.0064265 9.718e-04 0.7143
Erysipelotrichales patient FALSE . 3 3.388e-02 0.0366202 2.731e-02 1.0000
Erysipelotrichales patient FALSE . 4 5.830e-02 0.0980216 5.452e-03 1.0000
Erysipelotrichales patient TRUE . 1 9.306e-03 0.0089180 8.445e-03 0.8462
Erysipelotrichales patient TRUE . 2 6.841e-03 0.0099875 3.901e-03 1.0000
Erysipelotrichales patient TRUE . 3 7.867e-03 0.0102408 5.726e-03 1.0000
Erysipelotrichales patient TRUE . 4 6.194e-03 0.0044215 4.538e-03 1.0000
Selenomonadales 1 1 2.523e-02 0.0595107 2.399e-03 0.9444
Selenomonadales 1 2 1.364e-02 0.0178986 1.364e-02 1.0000
Selenomonadales patient FALSE . 1 3.888e-03 0.0064056 1.009e-03 0.9000
Selenomonadales patient FALSE . 2 5.700e-02 0.0820208 6.478e-03 0.8571
Selenomonadales patient FALSE . 3 2.475e-02 0.0330100 1.083e-02 0.8333
Selenomonadales patient FALSE . 4 1.034e-02 0.0097121 9.060e-03 1.0000
Selenomonadales patient TRUE . 1 7.876e-03 0.0164843 1.992e-03 0.9231
Selenomonadales patient TRUE . 2 1.201e-02 0.0219971 2.560e-03 0.7000
Selenomonadales patient TRUE . 3 5.929e-03 0.0061419 4.186e-03 0.7500
Selenomonadales patient TRUE . 4 5.040e-03 0.0067788 2.231e-04 0.8571
Enterobacteriales 1 1 1.802e-02 0.0724385 3.219e-04 0.6111
Enterobacteriales 1 2 3.389e-03 0.0030767 3.389e-03 1.0000
Enterobacteriales patient FALSE . 1 1.535e-02 0.0459956 1.286e-04 0.5000
Enterobacteriales patient FALSE . 2 2.289e-03 0.0052191 4.125e-04 0.7143
Enterobacteriales patient FALSE . 3 1.166e-02 0.0226829 3.416e-03 0.8333
Enterobacteriales patient FALSE . 4 2.257e-03 0.0031829 4.479e-04 0.6667
Enterobacteriales patient TRUE . 1 1.960e-02 0.0657493 0.000e+00 0.4615
Enterobacteriales patient TRUE . 2 2.773e-03 0.0063255 1.966e-04 0.6000
Enterobacteriales patient TRUE . 3 2.961e-03 0.0070945 3.210e-04 0.6250
Enterobacteriales patient TRUE . 4 2.872e-02 0.0346364 1.756e-02 0.7143
Burkholderiales 1 1 1.205e-02 0.0275947 2.167e-03 0.8333
Burkholderiales 1 2 0.000e+00 0.0000000 0.000e+00 0.0000
Burkholderiales patient FALSE . 1 8.138e-03 0.0116529 2.577e-03 1.0000
Burkholderiales patient FALSE . 2 1.182e-02 0.0157578 6.155e-03 0.5714
Burkholderiales patient FALSE . 3 1.331e-03 0.0030802 0.000e+00 0.3333
Burkholderiales patient FALSE . 4 1.559e-02 0.0333630 3.219e-04 0.5000
Burkholderiales patient TRUE . 1 9.798e-03 0.0169181 1.809e-03 0.6154
Burkholderiales patient TRUE . 2 1.217e-02 0.0192170 0.000e+00 0.4000
Burkholderiales patient TRUE . 3 8.794e-03 0.0162850 0.000e+00 0.2500
Burkholderiales patient TRUE . 4 6.077e-03 0.0145892 0.000e+00 0.4286
Unclassified_Bacteria 1 1 1.364e-02 0.0114079 1.054e-02 1.0000
Unclassified_Bacteria 1 2 2.617e-02 0.0324305 2.617e-02 1.0000
Unclassified_Bacteria patient FALSE . 1 1.480e-02 0.0271664 4.448e-03 1.0000
Unclassified_Bacteria patient FALSE . 2 2.186e-03 0.0022072 1.388e-03 0.8571
Unclassified_Bacteria patient FALSE . 3 5.270e-03 0.0038238 3.444e-03 1.0000
Unclassified_Bacteria patient FALSE . 4 4.114e-03 0.0042506 2.007e-03 1.0000
Unclassified_Bacteria patient TRUE . 1 3.807e-03 0.0041644 2.257e-03 0.9231
Unclassified_Bacteria patient TRUE . 2 2.145e-03 0.0018121 2.054e-03 0.9000
Unclassified_Bacteria patient TRUE . 3 1.982e-03 0.0015373 1.345e-03 1.0000
Unclassified_Bacteria patient TRUE . 4 5.219e-03 0.0083704 1.399e-03 1.0000
Unclassified_Firmicutes 1 1 8.036e-03 0.0109414 3.210e-03 1.0000
Unclassified_Firmicutes 1 2 1.259e-02 0.0057974 1.259e-02 1.0000
Unclassified_Firmicutes patient FALSE . 1 2.802e-03 0.0040007 1.172e-03 1.0000
Unclassified_Firmicutes patient FALSE . 2 1.103e-02 0.0126588 7.867e-03 0.7143
Unclassified_Firmicutes patient FALSE . 3 1.975e-02 0.0247764 1.006e-02 1.0000
Unclassified_Firmicutes patient FALSE . 4 7.886e-03 0.0084795 4.579e-03 1.0000
Unclassified_Firmicutes patient TRUE . 1 2.142e-03 0.0029892 6.030e-04 0.7692
Unclassified_Firmicutes patient TRUE . 2 1.606e-03 0.0020737 5.869e-04 0.8000
Unclassified_Firmicutes patient TRUE . 3 1.509e-03 0.0012706 1.063e-03 1.0000
Unclassified_Firmicutes patient TRUE . 4 9.570e-04 0.0012571 6.692e-04 0.8571
Pasteurellales 1 1 9.234e-04 0.0012789 4.058e-04 0.6667
Pasteurellales 1 2 4.910e-03 0.0069438 4.910e-03 0.5000
Pasteurellales patient FALSE . 1 1.112e-03 0.0025630 0.000e+00 0.4000
Pasteurellales patient FALSE . 2 2.033e-03 0.0023341 1.650e-03 0.8571
Pasteurellales patient FALSE . 3 1.210e-02 0.0213920 0.000e+00 0.3333
Pasteurellales patient FALSE . 4 1.837e-02 0.0397949 1.708e-03 0.8333
Pasteurellales patient TRUE . 1 1.341e-04 0.0002383 0.000e+00 0.3077
Pasteurellales patient TRUE . 2 8.641e-04 0.0017855 4.263e-05 0.5000
Pasteurellales patient TRUE . 3 3.303e-03 0.0048055 1.166e-03 0.6250
Pasteurellales patient TRUE . 4 2.506e-02 0.0656216 2.231e-04 0.7143
Bifidobacteriales 1 1 1.565e-02 0.0449947 1.592e-03 0.7778
Bifidobacteriales 1 2 6.749e-03 0.0089723 6.749e-03 1.0000
Bifidobacteriales patient FALSE . 1 1.552e-03 0.0032111 1.985e-04 0.7000
Bifidobacteriales patient FALSE . 2 3.356e-04 0.0006091 0.000e+00 0.4286
Bifidobacteriales patient FALSE . 3 1.383e-03 0.0031773 9.832e-05 0.5000
Bifidobacteriales patient FALSE . 4 1.767e-03 0.0039194 9.250e-05 0.5000
Bifidobacteriales patient TRUE . 1 1.974e-03 0.0057152 3.015e-04 0.6154
Bifidobacteriales patient TRUE . 2 1.000e-03 0.0024048 1.473e-04 0.7000
Bifidobacteriales patient TRUE . 3 5.377e-03 0.0087820 9.066e-04 0.6250
Bifidobacteriales patient TRUE . 4 3.710e-03 0.0060044 5.198e-04 0.7143
Verrucomicrobiales 1 1 2.550e-03 0.0051198 0.000e+00 0.3889
Verrucomicrobiales 1 2 2.136e-02 0.0292859 2.136e-02 1.0000
Verrucomicrobiales patient FALSE . 1 6.661e-03 0.0120381 0.000e+00 0.4000
Verrucomicrobiales patient FALSE . 2 4.125e-04 0.0010915 0.000e+00 0.1429
Verrucomicrobiales patient FALSE . 3 1.873e-04 0.0004587 0.000e+00 0.1667
Verrucomicrobiales patient FALSE . 4 6.167e-05 0.0001510 0.000e+00 0.1667
Verrucomicrobiales patient TRUE . 1 1.355e-02 0.0485697 0.000e+00 0.3077
Verrucomicrobiales patient TRUE . 2 3.747e-04 0.0011850 0.000e+00 0.1000
Verrucomicrobiales patient TRUE . 3 8.617e-04 0.0024373 0.000e+00 0.1250
Verrucomicrobiales patient TRUE . 4 0.000e+00 0.0000000 0.000e+00 0.0000
Rhizobiales 1 1 6.352e-03 0.0060510 7.039e-03 0.8889
Rhizobiales 1 2 2.455e-03 0.0034719 2.455e-03 0.5000
Rhizobiales patient FALSE . 1 1.645e-03 0.0022707 7.732e-04 0.6000
Rhizobiales patient FALSE . 2 2.085e-03 0.0048003 3.915e-04 0.7143
Rhizobiales patient FALSE . 3 1.387e-04 0.0003398 0.000e+00 0.1667
Rhizobiales patient FALSE . 4 8.545e-04 0.0015338 1.558e-04 0.5000
Rhizobiales patient TRUE . 1 1.928e-03 0.0036381 1.941e-04 0.5385
Rhizobiales patient TRUE . 2 3.214e-03 0.0056686 2.445e-04 0.6000
Rhizobiales patient TRUE . 3 1.023e-03 0.0026629 0.000e+00 0.2500
Rhizobiales patient TRUE . 4 1.675e-03 0.0041942 0.000e+00 0.4286

(1.1.1.2.3.2.4.2.1.1.1) Figure 60. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar_stacked plot. Image file: plots/3237d130b33.svg.

(1.1.1.2.3.2.4.2.1.1.1) Figure 61. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/323271fa583.svg.

(1.1.1.2.3.2.4.2.1.1.1) Figure 62. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/3233964dfb4.svg.

(1.1.1.2.3.2.4.2.1.1.1) Figure 63. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/3237b16442c.svg.

(1.1.1.2.3.2.4.2.1.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.2.3.2.4.2.1.2.1) Figure 64. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/3232f4cd911.svg.

(1.1.1.2.3.2.4.2.1.2.1) Figure 65. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/32344a28c63.svg.

(1.1.1.2.3.2.4.2.1.2.1) Figure 66. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/32359243d63.svg.

(1.1.1.2.3.2.4.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.1.1.2.3.2.4.2.2.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.2.3.2.4.2.2.1.1) Figure 67. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/32314af8ea4.svg.

(1.1.1.2.3.2.4.2.2.1.1) Figure 68. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/3231fffff56.svg.

(1.1.1.2.3.2.4.2.2.1.1) Figure 69. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/323f0663e5.svg.

(1.1.1.2.3.2.4.2.2.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.2.3.2.4.2.2.2.1) Figure 70. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/3234ba87e3.svg.

(1.1.1.2.3.2.4.2.2.2.1) Figure 71. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/3232a8e6a04.svg.

(1.1.1.2.3.2.4.2.2.2.1) Figure 72. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/3236e4000f5.svg.

(1.1.1.2.3.2.5) Grouping variables Drug.Before.Diet,Sample.type.1
(1.1.1.2.3.2.6) Iterating over Abundance. profile sorting order
(1.1.1.2.3.2.6.1) Abundance. profile sorting order: average abundance
(1.1.1.2.3.2.6.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.1.1.2.3.2.6.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.1.1.2.3.2.6.2.1.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.2.3.2.6.2.1.1.0) Table 16. Data table used for plots. Data grouped by Drug.Before.Diet,Sample.type.1. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.2.3.2.6.2.1.1.0-32344dd42dd.1.1.1.2.3.2.6.2.1.1.csv

.record.id Drug.Before.Diet Sample.type.1 feature Abundance
SM1 DrugBefore_YES patient.before.diet Bacteroidales 7.837e-01
SM10 DrugBefore_YES patient.after.diet Bacteroidales 2.396e-01
SM100 DrugBefore_YES patient.after.diet Bacteroidales 5.483e-01
SM11 DrugBefore_YES patient.after.diet Bacteroidales 9.084e-01
SM12 DrugBefore_YES patient.before.diet Bacteroidales 9.279e-01
SM13 DrugBefore_NO patient.before.diet Bacteroidales 7.549e-01
SM14 DrugBefore_NO patient.before.diet Bacteroidales 6.361e-02
SM15 DrugBefore_YES control Bacteroidales 4.786e-01
SM16 DrugBefore_NO patient.after.diet Bacteroidales 3.910e-01
SM17 DrugBefore_YES patient.before.diet Bacteroidales 8.184e-01
SM18 DrugBefore_NO patient.after.diet Bacteroidales 7.195e-01
SM19 DrugBefore_NO patient.after.diet Bacteroidales 2.254e-01
SM2 DrugBefore_NO patient.before.diet Bacteroidales 8.870e-01
SM20 DrugBefore_NO control Bacteroidales 5.050e-01
SM21 DrugBefore_NO patient.before.diet Bacteroidales 5.680e-01
SM22 DrugBefore_YES patient.before.diet Bacteroidales 6.107e-01
SM23 DrugBefore_YES patient.after.diet Bacteroidales 2.816e-01
SM24 DrugBefore_NO patient.before.diet Bacteroidales 8.665e-01
SM25 DrugBefore_NO patient.after.diet Bacteroidales 4.540e-01
SM26 DrugBefore_NO control Bacteroidales 5.338e-01
SM28 DrugBefore_NO control Bacteroidales 2.662e-01
SM29 DrugBefore_YES patient.after.diet Bacteroidales 9.319e-01
SM3 DrugBefore_YES patient.after.diet Bacteroidales 3.066e-01
SM30 DrugBefore_YES patient.after.diet Bacteroidales 6.906e-02
SM31 DrugBefore_NO control Bacteroidales 5.821e-01
SM33 DrugBefore_YES patient.before.diet Bacteroidales 6.904e-01
SM35 DrugBefore_NO control Bacteroidales 6.847e-01
SM36 DrugBefore_NO patient.after.diet Bacteroidales 3.219e-04
SM37 DrugBefore_NO control Bacteroidales 4.112e-01
SM38 DrugBefore_YES patient.after.diet Bacteroidales 9.845e-01
SM39 DrugBefore_NO patient.before.diet Bacteroidales 9.342e-01
SM40 DrugBefore_NO patient.after.diet Bacteroidales 7.285e-01
SM41 DrugBefore_YES patient.before.diet Bacteroidales 5.559e-01
SM42 DrugBefore_NO patient.after.diet Bacteroidales 7.114e-01
SM43 DrugBefore_YES patient.after.diet Bacteroidales 7.229e-01
SM44 DrugBefore_NO control Bacteroidales 3.689e-01
SM45 DrugBefore_NO patient.after.diet Bacteroidales 0.000e+00
SM48 DrugBefore_NO control Bacteroidales 7.186e-01
SM49 DrugBefore_YES patient.before.diet Bacteroidales 9.322e-01
SM5 DrugBefore_YES patient.after.diet Bacteroidales 8.376e-01
SM50 DrugBefore_NO patient.after.diet Bacteroidales 0.000e+00
SM51 DrugBefore_YES patient.after.diet Bacteroidales 7.147e-01
SM52 DrugBefore_NO patient.before.diet Bacteroidales 9.827e-02
SM53 DrugBefore_YES patient.after.diet Bacteroidales 8.029e-01
SM54 DrugBefore_YES patient.after.diet Bacteroidales 8.090e-01
SM55 DrugBefore_NO control Bacteroidales 7.866e-01
SM56 DrugBefore_YES patient.after.diet Bacteroidales 7.317e-01
SM57 DrugBefore_YES patient.before.diet Bacteroidales 9.046e-01
SM58 DrugBefore_NO patient.after.diet Bacteroidales 7.692e-01
SM59 DrugBefore_NO patient.after.diet Bacteroidales 5.768e-02
SM60 DrugBefore_YES patient.after.diet Bacteroidales 8.475e-01
SM62 DrugBefore_YES patient.before.diet Bacteroidales 9.715e-01
SM63 DrugBefore_NO control Bacteroidales 6.518e-01
SM64 DrugBefore_YES patient.after.diet Bacteroidales 8.683e-01
SM65 DrugBefore_YES patient.after.diet Bacteroidales 3.741e-01
SM66 DrugBefore_NO control Bacteroidales 6.462e-01
SM67 DrugBefore_YES patient.after.diet Bacteroidales 9.138e-01
SM68 DrugBefore_NO patient.after.diet Bacteroidales 1.705e-01
SM69 DrugBefore_YES patient.after.diet Bacteroidales 8.374e-01
SM7 DrugBefore_NO control Bacteroidales 2.192e-01
SM70 DrugBefore_NO control Bacteroidales 5.637e-01
SM71 DrugBefore_YES patient.after.diet Bacteroidales 9.175e-01
SM72 DrugBefore_NO control Bacteroidales 2.778e-01
SM73 DrugBefore_NO patient.before.diet Bacteroidales 8.563e-01
SM74 DrugBefore_NO control Bacteroidales 9.231e-02
SM75 DrugBefore_NO patient.after.diet Bacteroidales 2.377e-03
SM76 DrugBefore_NO control Bacteroidales 8.224e-01
SM77 DrugBefore_YES patient.after.diet Bacteroidales 7.635e-01
SM79 DrugBefore_NO patient.after.diet Bacteroidales 8.495e-01
SM8 DrugBefore_NO patient.before.diet Bacteroidales 8.250e-01
SM81 DrugBefore_NO control Bacteroidales 0.000e+00
SM82 DrugBefore_YES patient.after.diet Bacteroidales 9.555e-01
SM83 DrugBefore_YES patient.before.diet Bacteroidales 8.254e-01
SM84 DrugBefore_YES patient.before.diet Bacteroidales 8.858e-01
SM86 DrugBefore_YES patient.after.diet Bacteroidales 2.792e-03
SM87 DrugBefore_YES patient.before.diet Bacteroidales 8.668e-01
SM88 DrugBefore_YES patient.after.diet Bacteroidales 8.385e-01
SM89 DrugBefore_NO control Bacteroidales 8.778e-01
SM9 DrugBefore_NO patient.after.diet Bacteroidales 6.635e-01
SM90 DrugBefore_NO patient.after.diet Bacteroidales 6.176e-01
SM91 DrugBefore_YES patient.after.diet Bacteroidales 7.223e-01
SM92 DrugBefore_NO patient.after.diet Bacteroidales 8.864e-01
SM93 DrugBefore_YES patient.before.diet Bacteroidales 7.781e-01
SM95 DrugBefore_NO control Bacteroidales 5.366e-01
SM96 DrugBefore_NO patient.before.diet Bacteroidales 6.376e-01
SM98 DrugBefore_NO patient.after.diet Bacteroidales 8.378e-01
SM99 DrugBefore_NO patient.after.diet Bacteroidales 6.951e-01
SM1 DrugBefore_YES patient.before.diet Clostridiales 1.709e-01
SM10 DrugBefore_YES patient.after.diet Clostridiales 7.097e-01
SM100 DrugBefore_YES patient.after.diet Clostridiales 4.044e-01
SM11 DrugBefore_YES patient.after.diet Clostridiales 6.923e-02
SM12 DrugBefore_YES patient.before.diet Clostridiales 6.299e-02
SM13 DrugBefore_NO patient.before.diet Clostridiales 1.670e-01
SM14 DrugBefore_NO patient.before.diet Clostridiales 3.018e-01
SM15 DrugBefore_YES control Clostridiales 4.844e-01
SM16 DrugBefore_NO patient.after.diet Clostridiales 5.717e-01
SM17 DrugBefore_YES patient.before.diet Clostridiales 1.038e-01
SM18 DrugBefore_NO patient.after.diet Clostridiales 9.552e-02
SM19 DrugBefore_NO patient.after.diet Clostridiales 7.154e-01
SM2 DrugBefore_NO patient.before.diet Clostridiales 2.821e-02
SM20 DrugBefore_NO control Clostridiales 4.550e-01
SM21 DrugBefore_NO patient.before.diet Clostridiales 3.925e-01
SM22 DrugBefore_YES patient.before.diet Clostridiales 2.891e-01
SM23 DrugBefore_YES patient.after.diet Clostridiales 1.659e-03
SM24 DrugBefore_NO patient.before.diet Clostridiales 8.129e-02
SM25 DrugBefore_NO patient.after.diet Clostridiales 5.006e-01
SM26 DrugBefore_NO control Clostridiales 2.131e-01
SM28 DrugBefore_NO control Clostridiales 6.583e-01
SM29 DrugBefore_YES patient.after.diet Clostridiales 5.931e-02
SM3 DrugBefore_YES patient.after.diet Clostridiales 6.225e-01
SM30 DrugBefore_YES patient.after.diet Clostridiales 6.076e-01
SM31 DrugBefore_NO control Clostridiales 3.188e-01
SM33 DrugBefore_YES patient.before.diet Clostridiales 4.996e-02
SM35 DrugBefore_NO control Clostridiales 1.664e-01
SM36 DrugBefore_NO patient.after.diet Clostridiales 7.193e-01
SM37 DrugBefore_NO control Clostridiales 4.996e-01
SM38 DrugBefore_YES patient.after.diet Clostridiales 1.115e-02
SM39 DrugBefore_NO patient.before.diet Clostridiales 4.334e-02
SM40 DrugBefore_NO patient.after.diet Clostridiales 1.535e-01
SM41 DrugBefore_YES patient.before.diet Clostridiales 1.723e-01
SM42 DrugBefore_NO patient.after.diet Clostridiales 2.559e-01
SM43 DrugBefore_YES patient.after.diet Clostridiales 1.955e-01
SM44 DrugBefore_NO control Clostridiales 5.344e-01
SM45 DrugBefore_NO patient.after.diet Clostridiales 0.000e+00
SM48 DrugBefore_NO control Clostridiales 2.252e-01
SM49 DrugBefore_YES patient.before.diet Clostridiales 5.216e-02
SM5 DrugBefore_YES patient.after.diet Clostridiales 9.120e-02
SM50 DrugBefore_NO patient.after.diet Clostridiales 7.065e-01
SM51 DrugBefore_YES patient.after.diet Clostridiales 1.970e-01
SM52 DrugBefore_NO patient.before.diet Clostridiales 6.445e-01
SM53 DrugBefore_YES patient.after.diet Clostridiales 1.491e-01
SM54 DrugBefore_YES patient.after.diet Clostridiales 1.726e-01
SM55 DrugBefore_NO control Clostridiales 1.877e-01
SM56 DrugBefore_YES patient.after.diet Clostridiales 2.125e-01
SM57 DrugBefore_YES patient.before.diet Clostridiales 8.819e-02
SM58 DrugBefore_NO patient.after.diet Clostridiales 1.200e-01
SM59 DrugBefore_NO patient.after.diet Clostridiales 7.978e-01
SM60 DrugBefore_YES patient.after.diet Clostridiales 6.399e-02
SM62 DrugBefore_YES patient.before.diet Clostridiales 2.529e-02
SM63 DrugBefore_NO control Clostridiales 2.766e-01
SM64 DrugBefore_YES patient.after.diet Clostridiales 7.026e-02
SM65 DrugBefore_YES patient.after.diet Clostridiales 5.640e-01
SM66 DrugBefore_NO control Clostridiales 3.152e-01
SM67 DrugBefore_YES patient.after.diet Clostridiales 7.164e-02
SM68 DrugBefore_NO patient.after.diet Clostridiales 5.874e-01
SM69 DrugBefore_YES patient.after.diet Clostridiales 1.229e-01
SM7 DrugBefore_NO control Clostridiales 6.268e-01
SM70 DrugBefore_NO control Clostridiales 3.025e-01
SM71 DrugBefore_YES patient.after.diet Clostridiales 5.366e-02
SM72 DrugBefore_NO control Clostridiales 1.571e-01
SM73 DrugBefore_NO patient.before.diet Clostridiales 9.994e-02
SM74 DrugBefore_NO control Clostridiales 7.925e-01
SM75 DrugBefore_NO patient.after.diet Clostridiales 8.122e-01
SM76 DrugBefore_NO control Clostridiales 1.502e-01
SM77 DrugBefore_YES patient.after.diet Clostridiales 1.921e-01
SM79 DrugBefore_NO patient.after.diet Clostridiales 1.412e-01
SM8 DrugBefore_NO patient.before.diet Clostridiales 1.294e-01
SM81 DrugBefore_NO control Clostridiales 3.292e-01
SM82 DrugBefore_YES patient.after.diet Clostridiales 2.914e-02
SM83 DrugBefore_YES patient.before.diet Clostridiales 1.565e-01
SM84 DrugBefore_YES patient.before.diet Clostridiales 5.785e-02
SM86 DrugBefore_YES patient.after.diet Clostridiales 8.889e-01
SM87 DrugBefore_YES patient.before.diet Clostridiales 7.040e-02
SM88 DrugBefore_YES patient.after.diet Clostridiales 1.247e-01
SM89 DrugBefore_NO control Clostridiales 6.822e-02
SM9 DrugBefore_NO patient.after.diet Clostridiales 7.939e-02
SM90 DrugBefore_NO patient.after.diet Clostridiales 2.991e-01
SM91 DrugBefore_YES patient.after.diet Clostridiales 2.006e-01
SM92 DrugBefore_NO patient.after.diet Clostridiales 8.090e-02
SM93 DrugBefore_YES patient.before.diet Clostridiales 1.938e-01
SM95 DrugBefore_NO control Clostridiales 3.756e-01
SM96 DrugBefore_NO patient.before.diet Clostridiales 2.363e-01
SM98 DrugBefore_NO patient.after.diet Clostridiales 5.983e-02
SM99 DrugBefore_NO patient.after.diet Clostridiales 2.487e-01
SM1 DrugBefore_YES patient.before.diet Lactobacillales 4.329e-04
SM10 DrugBefore_YES patient.after.diet Lactobacillales 4.240e-04
SM100 DrugBefore_YES patient.after.diet Lactobacillales 3.077e-04
SM11 DrugBefore_YES patient.after.diet Lactobacillales 6.567e-04
SM12 DrugBefore_YES patient.before.diet Lactobacillales 8.853e-05
SM13 DrugBefore_NO patient.before.diet Lactobacillales 0.000e+00
SM14 DrugBefore_NO patient.before.diet Lactobacillales 1.905e-01
SM15 DrugBefore_YES control Lactobacillales 1.557e-03
SM16 DrugBefore_NO patient.after.diet Lactobacillales 4.875e-03
SM17 DrugBefore_YES patient.before.diet Lactobacillales 1.241e-03
SM18 DrugBefore_NO patient.after.diet Lactobacillales 1.242e-02
SM19 DrugBefore_NO patient.after.diet Lactobacillales 1.388e-03
SM2 DrugBefore_NO patient.before.diet Lactobacillales 7.278e-02
SM20 DrugBefore_NO control Lactobacillales 2.955e-03
SM21 DrugBefore_NO patient.before.diet Lactobacillales 2.690e-03
SM22 DrugBefore_YES patient.before.diet Lactobacillales 3.071e-03
SM23 DrugBefore_YES patient.after.diet Lactobacillales 7.105e-01
SM24 DrugBefore_NO patient.before.diet Lactobacillales 6.431e-04
SM25 DrugBefore_NO patient.after.diet Lactobacillales 7.765e-03
SM26 DrugBefore_NO control Lactobacillales 7.612e-02
SM28 DrugBefore_NO control Lactobacillales 0.000e+00
SM29 DrugBefore_YES patient.after.diet Lactobacillales 0.000e+00
SM3 DrugBefore_YES patient.after.diet Lactobacillales 8.146e-03
SM30 DrugBefore_YES patient.after.diet Lactobacillales 7.637e-03
SM31 DrugBefore_NO control Lactobacillales 3.236e-03
SM33 DrugBefore_YES patient.before.diet Lactobacillales 7.868e-04

(1.1.1.2.3.2.6.2.1.1.1) Widget 15. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Drug.Before.Diet,Sample.type.1. Click to see HTML widget file in full window: ./1.1.1.2.3.2.6.2.1.1.1-3237c402688Dynamic.Pivot.Table.html

(1.1.1.2.3.2.6.2.1.1.1) Widget 16. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Drug.Before.Diet,Sample.type.1. Click to see HTML widget file in full window: ./1.1.1.2.3.2.6.2.1.1.1-32324500a52Dynamic.Pivot.Table.html

(1.1.1.2.3.2.6.2.1.1.1) Table 17. Summary table. Data grouped by Drug.Before.Diet,Sample.type.1. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.2.3.2.6.2.1.1.1-32354e16c95.1.1.1.2.3.2.6.2.1.1.csv

feature Drug.Before.Diet Sample.type.1 mean sd median incidence
Bacteroidales DrugBefore_NO control 5.024e-01 0.2463647 5.366e-01 0.9474
Bacteroidales DrugBefore_NO patient.after.diet 4.621e-01 0.3370960 6.176e-01 0.8947
Bacteroidales DrugBefore_NO patient.before.diet 6.491e-01 0.3202663 7.900e-01 1.0000
Bacteroidales DrugBefore_YES control 4.786e-01 NA 4.786e-01 1.0000
Bacteroidales DrugBefore_YES patient.after.diet 6.772e-01 0.2897179 8.029e-01 1.0000
Bacteroidales DrugBefore_YES patient.before.diet 8.116e-01 0.1269502 8.254e-01 1.0000
Clostridiales DrugBefore_NO control 3.501e-01 0.1967236 3.152e-01 1.0000
Clostridiales DrugBefore_NO patient.after.diet 3.655e-01 0.2895083 2.559e-01 0.9474
Clostridiales DrugBefore_NO patient.before.diet 2.124e-01 0.1911962 1.482e-01 1.0000
Clostridiales DrugBefore_YES control 4.844e-01 NA 4.844e-01 1.0000
Clostridiales DrugBefore_YES patient.after.diet 2.354e-01 0.2469199 1.491e-01 1.0000
Clostridiales DrugBefore_YES patient.before.diet 1.149e-01 0.0761953 8.819e-02 1.0000
Lactobacillales DrugBefore_NO control 2.312e-02 0.0646430 8.803e-04 0.8947
Lactobacillales DrugBefore_NO patient.after.diet 5.914e-02 0.2282866 1.578e-03 0.9474
Lactobacillales DrugBefore_NO patient.before.diet 2.930e-02 0.0610415 1.463e-03 0.9000
Lactobacillales DrugBefore_YES control 1.557e-03 NA 1.557e-03 1.0000
Lactobacillales DrugBefore_YES patient.after.diet 2.993e-02 0.1418059 4.461e-04 0.8800
Lactobacillales DrugBefore_YES patient.before.diet 1.230e-03 0.0015603 4.329e-04 0.8462
Erysipelotrichales DrugBefore_NO control 9.885e-03 0.0161712 4.054e-03 0.8947
Erysipelotrichales DrugBefore_NO patient.after.diet 3.073e-02 0.0598480 2.782e-03 0.8947
Erysipelotrichales DrugBefore_NO patient.before.diet 4.869e-02 0.1197808 9.058e-03 1.0000
Erysipelotrichales DrugBefore_YES control 7.360e-03 NA 7.360e-03 1.0000
Erysipelotrichales DrugBefore_YES patient.after.diet 6.988e-03 0.0085635 4.769e-03 1.0000
Erysipelotrichales DrugBefore_YES patient.before.diet 9.306e-03 0.0089180 8.445e-03 0.8462
Selenomonadales DrugBefore_NO control 2.533e-02 0.0578128 3.094e-03 0.9474
Selenomonadales DrugBefore_NO patient.after.diet 3.208e-02 0.0546661 8.414e-03 0.8947
Selenomonadales DrugBefore_NO patient.before.diet 3.888e-03 0.0064056 1.009e-03 0.9000
Selenomonadales DrugBefore_YES control 7.077e-05 NA 7.077e-05 1.0000
Selenomonadales DrugBefore_YES patient.after.diet 8.110e-03 0.0146492 3.814e-03 0.7600
Selenomonadales DrugBefore_YES patient.before.diet 7.876e-03 0.0164843 1.992e-03 0.9231
Enterobacteriales DrugBefore_NO control 1.743e-02 0.0704395 4.137e-04 0.6842
Enterobacteriales DrugBefore_NO patient.after.diet 5.238e-03 0.0132252 8.125e-04 0.7368
Enterobacteriales DrugBefore_NO patient.before.diet 1.535e-02 0.0459956 1.286e-04 0.5000
Enterobacteriales DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.0000
Enterobacteriales DrugBefore_YES patient.after.diet 1.010e-02 0.0216814 3.134e-04 0.6400
Enterobacteriales DrugBefore_YES patient.before.diet 1.960e-02 0.0657493 0.000e+00 0.4615
Burkholderiales DrugBefore_NO control 1.141e-02 0.0269593 2.142e-03 0.7895
Burkholderiales DrugBefore_NO patient.after.diet 9.697e-03 0.0207667 0.000e+00 0.4737
Burkholderiales DrugBefore_NO patient.before.diet 8.138e-03 0.0116529 2.577e-03 1.0000
Burkholderiales DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.0000
Burkholderiales DrugBefore_YES patient.after.diet 9.385e-03 0.0166011 0.000e+00 0.3600
Burkholderiales DrugBefore_YES patient.before.diet 9.798e-03 0.0169181 1.809e-03 0.6154
Unclassified_Bacteria DrugBefore_NO control 1.534e-02 0.0138827 1.188e-02 1.0000
Unclassified_Bacteria DrugBefore_NO patient.after.diet 3.769e-03 0.0035311 2.600e-03 0.9474
Unclassified_Bacteria DrugBefore_NO patient.before.diet 1.480e-02 0.0271664 4.448e-03 1.0000
Unclassified_Bacteria DrugBefore_YES control 6.298e-03 NA 6.298e-03 1.0000
Unclassified_Bacteria DrugBefore_YES patient.after.diet 2.953e-03 0.0046391 1.726e-03 0.9600
Unclassified_Bacteria DrugBefore_YES patient.before.diet 3.807e-03 0.0041644 2.257e-03 0.9231
Unclassified_Firmicutes DrugBefore_NO control 8.481e-03 0.0108170 3.610e-03 1.0000
Unclassified_Firmicutes DrugBefore_NO patient.after.diet 1.279e-02 0.0164090 7.867e-03 0.8947
Unclassified_Firmicutes DrugBefore_NO patient.before.diet 2.802e-03 0.0040007 1.172e-03 1.0000
Unclassified_Firmicutes DrugBefore_YES control 8.704e-03 NA 8.704e-03 1.0000
Unclassified_Firmicutes DrugBefore_YES patient.after.diet 1.393e-03 0.0015992 7.834e-04 0.8800
Unclassified_Firmicutes DrugBefore_YES patient.before.diet 2.142e-03 0.0029892 6.030e-04 0.7692
Pasteurellales DrugBefore_NO control 1.392e-03 0.0023896 4.546e-04 0.6842
Pasteurellales DrugBefore_NO patient.after.diet 1.037e-02 0.0248637 1.174e-03 0.6842
Pasteurellales DrugBefore_NO patient.before.diet 1.112e-03 0.0025630 0.000e+00 0.4000
Pasteurellales DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.0000
Pasteurellales DrugBefore_YES patient.after.diet 8.419e-03 0.0346081 1.554e-04 0.6000
Pasteurellales DrugBefore_YES patient.before.diet 1.341e-04 0.0002383 0.000e+00 0.3077
Bifidobacteriales DrugBefore_NO control 1.554e-02 0.0437231 1.599e-03 0.8421
Bifidobacteriales DrugBefore_NO patient.after.diet 1.118e-03 0.0027562 0.000e+00 0.4737
Bifidobacteriales DrugBefore_NO patient.before.diet 1.552e-03 0.0032111 1.985e-04 0.7000
Bifidobacteriales DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.0000
Bifidobacteriales DrugBefore_YES patient.after.diet 3.159e-03 0.0061111 2.231e-04 0.6800
Bifidobacteriales DrugBefore_YES patient.before.diet 1.974e-03 0.0057152 3.015e-04 0.6154
Verrucomicrobiales DrugBefore_NO control 4.665e-03 0.0103270 0.000e+00 0.4737
Verrucomicrobiales DrugBefore_NO patient.after.diet 2.306e-04 0.0006964 0.000e+00 0.1579
Verrucomicrobiales DrugBefore_NO patient.before.diet 6.661e-03 0.0120381 0.000e+00 0.4000
Verrucomicrobiales DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.0000
Verrucomicrobiales DrugBefore_YES patient.after.diet 4.256e-04 0.0015416 0.000e+00 0.0800
Verrucomicrobiales DrugBefore_YES patient.before.diet 1.355e-02 0.0485697 0.000e+00 0.3077
Rhizobiales DrugBefore_NO control 5.628e-03 0.0058660 4.910e-03 0.8421
Rhizobiales DrugBefore_NO patient.after.diet 1.082e-03 0.0030119 0.000e+00 0.4737
Rhizobiales DrugBefore_NO patient.before.diet 1.645e-03 0.0022707 7.732e-04 0.6000
Rhizobiales DrugBefore_YES control 1.231e-02 NA 1.231e-02 1.0000
Rhizobiales DrugBefore_YES patient.after.diet 2.082e-03 0.0044127 0.000e+00 0.4400
Rhizobiales DrugBefore_YES patient.before.diet 1.928e-03 0.0036381 1.941e-04 0.5385

(1.1.1.2.3.2.6.2.1.1.1) Figure 73. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar_stacked plot. Image file: plots/3235dd63030.svg.

(1.1.1.2.3.2.6.2.1.1.1) Figure 74. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/32371ffad79.svg.

(1.1.1.2.3.2.6.2.1.1.1) Figure 75. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/3236f190af1.svg.

(1.1.1.2.3.2.6.2.1.1.1) Figure 76. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/32310531dc8.svg.

(1.1.1.2.3.2.6.2.1.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.2.3.2.6.2.1.2.1) Figure 77. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/32346bd37a4.svg.

(1.1.1.2.3.2.6.2.1.2.1) Figure 78. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/32319cb0224.svg.

(1.1.1.2.3.2.6.2.1.2.1) Figure 79. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/3233bfad20f.svg.

(1.1.1.2.3.2.6.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.1.1.2.3.2.6.2.2.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.2.3.2.6.2.2.1.1) Figure 80. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/3233452e2b8.svg.

(1.1.1.2.3.2.6.2.2.1.1) Figure 81. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/3234e1c3c3a.svg.

(1.1.1.2.3.2.6.2.2.1.1) Figure 82. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/32320085755.svg.

(1.1.1.2.3.2.6.2.2.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.2.3.2.6.2.2.2.1) Figure 83. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/323599d35c2.svg.

(1.1.1.2.3.2.6.2.2.2.1) Figure 84. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/3237ec60f21.svg.

(1.1.1.2.3.2.6.2.2.2.1) Figure 85. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/3233c276a7b.svg.

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